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Wednesday, December 9, 2009

R1*-M173 Chromosomes in Africa - II

On another matter of African haplogroup R chromosomes...

As of Dec 4, 2009, the following was released by Molecular Anthropology in the Genomic Era team which oversaw the 4th International conference of the series on DNA polymorphisms in human populations that took place at University La Sapienza - Rome from December 3 through to 5, 2009:

Human Y chromosomes belonging to haplogroup R-P25 are quite rare in Africa, being found mainly in Asia and Europe. However, a group of P25 Y chromosomes that are not defined by the presence of a downstream derived marker (the paragroup R-P25*) are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25* chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back-migration in prehistoric times. Here we describe six new mutations that define the relationships among the African R-P25* Y chromosomes and between these African chromosomes and previously reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R-P25 haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25*, about half of the few European/west Asian R-P25*, and the R-M18 chromosomes. A world-wide phylogeographic analysis of the R-P25 haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in more than 1,800 males from 69 African populations, revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic speaking groups from North Africa. The R-V88 coalescence time was estimated at 9,200-5,600 kya, in the early-mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin.

Cruciani is known for making observations that don't exactly match up with what his actual DNA results show. The present author pointed this out on this site with both R1*-M173 chromosomes, E-M78 clusters and E-M34. So, the present author now reiterates what's wrong with his so-called "Asia-to-Africa back migration", which he seems bent on promoting, since otherwise would implicate European ancestry directly from Africa, which is known to get Eurocentrists' and closet-Eurocentrists' pants in a bunch.

Previously, when Cruciani (2002) thought he had come up with undifferentiated, upstream Hg R1* chromosomes, he considered it a possibility that this could be suggestive of African origin, since the African counterparts were phylogenetically more basal than his non-African sample collection; yet, this didn't phase him to entertain the alternative then, about back-migration to Africa, predicated on a flimsy case about Hg R, in its entirety as a family, not being as diverse in Africa as it appears to be in Asia. At the time, this was essentially Cruciani's sole argument for his preference of a back-migration scenario, which obviously contradicted the fact then, that his African samples were the ONLY ones which tested positive for the most basal R markers.

So now, he comes up with new markers, and tries to see if he can solidify his earlier rather debatable, if not flimsy, position. But even here, having sampled a number of Chadic-speaking populations in the central Sahel as a gesture of applying fine-tooth combing to the DNA sequencing of the Hg R chromosomes, particularly the perplexingly-unique African examples, he points out that the Hg R chromosomes bearing the "new mutations" he tested for are still more prevalent in Africa, and rarer in non-African areas. Yet, Cruciani wants to convince us that this is some sort of unequivocal proof that Africans must have attained it from back-migration, and he tries to reinforce this effort, by invoking early Holocene estimation dates. Also, contrary to Cruciani's mindset, it is not necessary for *all* the sub-clades of K to emerge in Africa, in order for the origin of K-M9 on the continent to be probable. Hg K's most immediate descendants like Hgs T, K1, K2...etc do not form monophyletic branching with respect to one another, but each of them form their own distinctive branch from the ancestral K-M9 node. Nor is it even necessary for the M9 mutation to have emerged in Africa, in order for R to emerge in Africa; humans are not static creatures. All that is needed, is for the P clade to have been present in Africa at some point in time. To the present author's knowledge, P has not been uncovered as a standalone clade [lacking downstream markers] anywhere. However, it is interesting to note that African R1*-M173 chromosomes were previously tested for the P25 mutation, and came up negative. What does this then mean? It means that while Africans carried rare Hg R1 chromosomes bearing the P25 marker, they also carried examples without the P25 marker [see Hassan et al. 2008, for example]. In other words, African R1-bearing chromosomes aren't homogeneous as Cruciani would perhaps like us to believe.

Furthermore, as the present author has noted here and elsewhere before,...

Interestingly, upon revisiting Wood et al. (2005), it should be pointed out that paraphyletic clade of R*-M207 was detected amongst some "Afro-Asiatic" African groups, along with the paraphyletic clade R1*-M173 [it is worth noting that Wood et al. implicate the Egyptian sample here as something other than that of Semitic speakers (Arabic)], while some Niger-Congo groups — though in small frequencies [pooled] —tested positive for the paraphyletic R1b*, lacking the established downstream R1b markers. Henceforth, R*-M207, lacking downstream mutations have been identified in African groups via this study; and yes, the basic nodes of all presently known Hg R's downstream clades had been accounted for, which means that R*, as predicted above, is NOT relegated to the Indian sub-continent. All in all, this suggests that African Hg R pool is actually more diverse than many seem to think.

So once again, African R-bearing chromosomes lacking the P25 marker have been identified, whereas Cruciani's Hg R chromosomes all appeared to have tested positive for P25; his samples bearing the R-positive chromosomes only differed from subsequentdownstream markers - presumably aside from one or more of those "new mutations" that Cruciani claims he had used in his DNA sequencing. African chromosomes transcend even the ancestral Hg R1* marker; the paraphyletic R* is also implicated, which is ancestral to R1* marker!

...but the present author has a hunch that Cruciani isn't done fine-combing Hg R chromosomes just yet, if he is to unequivocally prove that back-migration scenario he seems to so desire. So, watch this space, and please go over the cited R1*-M173 link(s) again, as it is constantly updated!
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References*

What is meant by "his African samples were the ONLY ones which tested positive for the most basal R markers"? Please explain this to me.

It means that at the time of the study in question, only the African samples showed up chromosomes that did not have younger unique event singular mutations that characterize sub-clades of the larger macro-haplogroup. This would make the African examples then, phylogenetically the oldest examples amongst the bunch studied.

Even today, Africans carry paraphyletic examples that are essentially non-existent in either Europe or the "Middle East". This is why Cruciani's efforts to pass off African hg R chromosomes as though they were the product of some homogeneous demographic event presents a rather humerous, if not entertaining, spectacle. Rare African hg R chromosomes are considerably diverse to be written off as the product of some simple one-time type scenario migratory event.

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